The NCI Laboratory of Genomic Diversity has identified AIDS restriction genes (ARGs) that affect the susceptibility of HIV-exposed individuals to viral infection or influence the rate that HIV-infected individuals progress to AIDS or death. In order to facilitate the discovery of new ARGs, a program named ARG Analysis was developed for the analysis of associations of genotypes from diallelic markers with HIV/AIDS-related outcomes. The statistical tests performed include categorical analyses of infection status and disease progression as well as survival analyses using the Cox proportional hazards model. The categorical analyses may be stratified by race. A goodness of fit test has been introduced that tests whether allele or genotype frequencies in defined disease categories differ significantly from overall frequencies. The program runs on a Linux-based computing cluster at the NCI-Frederick Advanced Biomedical Computing Center (ABCC) allowing the rapid analysis of large numbers of genotypes. It may be invoked either by submitting a batch job using the Portable Batch System (PBS) or through a web interface. The output consists of tables containing detailed results that are stored in a MySQL database. Other programs that produce a wide variety of reports can assess these tables. The ARG Array program displays the levels of significance or the strength of associations as color-coded squares allowing the results from a large number of tests to be displayed on a single page. More details are found in the ARG Tracks report that contains six pages of tables and graphs for each marker. The ARG Ranks program identifies markers that are most likely to be true ARGs using several ranking methods, and ARG Map graphically displays the ranks from each ranking method.